Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FLI1

Cell type

Cell type Class
Neural
Cell type
SK-N-MC
Primary Tissue
Brain
Site of Extraction
Brain
Tissue Diagnosis
neuroepithelioma

Attributes by original data submitter

Sample

source_name
FLI1 ChIP in SKNMC transduced with KRAB-ZFA7
chip antibody
FLI1 antibody (Abcam, cat# ab15289, lot# GR3229309-6)
cell line
SKNMC
treatment
transduced with KRAB-ZFA7

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, chromatin from 1% formaldehyde-fixed cells were fragmented to 200-500 bps by sonication for 5-6 mins using the Branson sonifer SFX250 RNA-seq:Single-end libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) and TruSeq RNA Single Indexes, pooled, and sequenced using an NextSeq500. ChIP-seq: Sequencing libraries were prepared with 3 ng of each H3K27Ac ChIP DNA and input sample using SMARTer ThruPLEX DNA-seq kit (Takara, Cat# R400675). Libraries were sequenced with single-end (SE) 75 cycles on an Illumina Nextseq 500 system

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
27568567
Reads aligned (%)
98.0
Duplicates removed (%)
15.8
Number of peaks
55720 (qval < 1E-05)

hg19

Number of total reads
27568567
Reads aligned (%)
97.4
Duplicates removed (%)
16.6
Number of peaks
55688 (qval < 1E-05)

Base call quality data from DBCLS SRA